Variant report

Variant	rs6825852
Chromosome Location	chr4:85662060-85662061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11725121	0.80[EUR][1000 genomes]
rs12500519	0.82[EUR][1000 genomes]
rs12502294	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12502409	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12511112	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13118671	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1484661	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1508670	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs16995920	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17009317	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs17009334	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2218323	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs35190829	0.81[EUR][1000 genomes]
rs36036245	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6816534	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6829807	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6838727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6858666	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.82[EUR][1000 genomes]
rs7685537	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7695054	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6825852	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
2	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
4	chr4:85620800-85663400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85629200-85662400	Weak transcription	Colonic Mucosa	Colon
6	chr4:85633400-85667800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:85640200-85663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:85642800-85668000	Weak transcription	Spleen	Spleen
10	chr4:85642800-85678000	Weak transcription	Gastric	stomach
11	chr4:85646400-85663400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:85648000-85676200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:85651000-85671400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:85651000-85673000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:85651000-85673200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:85651000-85676800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:85651000-85678600	Strong transcription	Placenta	Placenta
18	chr4:85651200-85664400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:85652200-85664000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:85652200-85664800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr4:85652200-85665000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:85652200-85665000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:85652200-85665200	Strong transcription	Adipose Nuclei	Adipose
24	chr4:85652200-85670000	Strong transcription	Liver	Liver
25	chr4:85652200-85678400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:85652200-85678400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:85652200-85679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:85652400-85664800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:85652400-85665000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:85652400-85666600	Strong transcription	HUVEC	blood vessel
31	chr4:85652400-85679200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:85652600-85664000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr4:85652600-85664600	Strong transcription	Fetal Lung	lung
34	chr4:85652600-85664800	Strong transcription	NH-A	brain
35	chr4:85652600-85665000	Strong transcription	Brain Anterior Caudate	brain
36	chr4:85652600-85671600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:85652600-85678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:85652600-85678600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:85653200-85667000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:85653600-85664400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:85654800-85663200	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:85655000-85668400	Weak transcription	Fetal Brain Male	brain
43	chr4:85655600-85664800	Strong transcription	HepG2	liver
44	chr4:85655800-85665200	Strong transcription	Fetal Kidney	kidney
45	chr4:85656200-85663600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr4:85656200-85664200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:85656400-85664800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:85656400-85664800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr4:85656600-85665000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:85656800-85672000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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